Publications

Selected Publications

  • Chu P#, Zhu J#, Ma Z, Fu X*. (2025)Colony pattern multistability emerges from a bistable switch. Proceedings of the National Academy of Sciences. 122(14):e2424112122. doi:10.1073/pnas.2424112122
  • Zhang Y, Hu Q, Su Y, Chu P, Wei T, Li X, Liu C, Fu X.* (2025) Navigated range expansion promotes migratory culling. Proceedings of the National Academy of Sciences.121(50):e2408303121. doi:10.1073/pnas.2408303121
  • Zhu J.#, Chu P.#, Fu X.* (2023) Unbalanced response to growth variations reshapes the cell fate decision landscape. Nature Chemical Biology 19:1097-1104. doi:10.1038/s41589-023-01346-x
  • Luo L.#, Bai Y.#, Fu X.* (2023) Stochastic threshold in cell size control. Physical Review Research 5:013173. doi:10.1103/PhysRevResearch.5.013173
  • Bai Y.#, He C.#, Chu P., Long J., Li X., Fu X.* (2021) Spatial modulation of individual behaviors enables an ordered structure of diverse phenotypes during bacterial group migration. eLife 10, https://elifesciences.org/articles/67316 [Dowload]

Publications

2025

Zhu J.#, Chu P.#, Fu X.* (2025). Understanding the development of bacterial colony: Physiology, new technology, and modeling. Quantitative Biology, 13(4), e95. https://doi.org/10.1002/qub2.95

Pan, D., Chu, P., Fu, X., Wen, D., Song, H., Bai, S., & Guo, X. (2025). Elucidating the underlying mechanism of the bactericidal effect facilitated by a crucial flagellar protein under high-voltage electrostatic conditions. Journal of Hazardous Materials, 491, 137963. https://doi.org/10.1016/j.jhazmat.2025.137963

Li S.#, Ma Z.#, Yu Y.#, Wang J., Shen Y., Cui X., Fu X., Huang S.* (2025) Coma pattern-based autofocusing unlocks superior performance in unravelling single-cell dynamics during bacterial cold shock response. BioRXiv. doi:10.1101/2024.10.15.618375

Wen L.#, Bai Y.#, Lan Y., Shen Y., She X., Dong P., Wang T., Fu X.*, Huang S.* (2025) Strong segregation promotes self-destructive cooperation. ISME Journal 16:wraf043. doi:10.1093/ismejo/wraf043

Yuan H.#, Bai Y., Fu X.* A global resource constrained model to predict metabolic flux dynamics in fluctuating environments. BioRXiv. doi:10.1101/2024.617971

Chu P#, Zhu J#, Ma Z, Fu X.* Colony pattern multistability emerges from a bistable switch. Proceedings of the National Academy of Sciences. 2025 Apr 8;122(14):e2424112122. doi:10.1073/pnas.2424112122

2024

Zhang Y, Hu Q, Su Y, Chu P, Wei T, Li X, Liu C, Fu X.* Navigated range expansion promotes migratory culling. Proceedings of the National Academy of Sciences. 2024 Dec 10;121(50):e2408303121. doi:10.1073/pnas.2408303121

Li Y., Fu X., Zhang X. (2024) A Brief Overview of Synthetic Biology. China Biotechnology 44(1):52-60.

Yuan H.#, Bai Y.#, Li X, Fu X. (2024) Cross-regulation between proteome reallocation and metabolic flux redistribution governs bacterial growth transition kinetics. Metabolic Engineering 82:60-68. doi:10.1016/j.ymben.2024.01.003

2023

Zhu J.#, Chu P.#, Fu X.* (2023) Unbalanced response to growth variations reshapes the cell fate decision landscape. Nature Chemical Biology 19:1097-1104. doi:10.1038/s41589-023-01346-x

Luo L.#, Bai Y.#, Fu X. (2023) Stochastic threshold in cell size control. Physical Review Research 5:013173. doi:10.1103/PhysRevResearch.5.013173

2022

Wei T.#, Lai W.#, Chen Q.#, Zhang Y.#, Sun C., He X., Zhao G., Fu X.*, Liu C.* (2022) Exploiting spatial dimensions to enable parallelized continuous directed evolution. Molecular Systems Biology 18:e10934. doi:10.15252/msb.202210934

Li Y., Fu X., Du L. (2022) Regulating the commercialization of cell-cultured meat: practices in selected jurisdictions and their implications for China. Synthetic Biology Journal 3(1):209-223.

Chu Y.#, Guo C.#, Cui D., Fu X., Ma Y.* (2022) DeephageTP: a convolutional neural network framework for identifying phage-specific proteins from metagenomic sequencing data. PeerJ 10:e13404. doi:10.7717/peerj.13404

2021

Bai Y.#, He C.#, Chu P., Long J., Li X., Fu X.* (2021) Spatial modulation of individual behaviors enables an ordered structure of diverse phenotypes during bacterial group migration. eLife 10, e67316.

Liu W., Tokuyasu, A. T., Fu X., Liu C. (2021) The spatial organization of microbial communities during range expansion. Current Opinion in Microbiology, 63, 109-116.

Luo L.#, Bai Y.#, Fu X. (2021) Master equation approach to the stochastic accumulation dynamics of bacterial cell cycle. New J. Phys. 23, 083029. DOI:10.1088/1367-2630/ac1976.

Chu P., Zhu J., Huang W., Liu C., Fu X.* (2021) Host-circuit coupling: toward a new framework for genetic circuit design. Synthetic Biology Journal. 2(1): 91-105.

Ma W., Wei T., Fu X., Li X. (2021) Quantitative engineering biology in the tumor. Chinese Science Bulletin, 66(3): 319-328.

Su Y.#, Bai Y., Qi F., Zhang Y., Fu X.* (2021) Spatiotemporal dynamics of bacterial collective migration. Chinese Science Bulletin, 66(3): 264-272.

2020

Xiang Y.#, Wen H., Yu Y., Li M., Fu X., Huang, S.* (2020) Gut-on-chip: Recreating human intestine in vitro. Journal of Tissue Engineering. DOI:10.1177/2041731420965318.

Zheng H.#, Bai Y.#, Jiang M.#, Tokuyasu T., Huang X., Zhong F., Wu Y., Fu X., Kleckner N., Hwa T., Liu C.* (2020) General quantitative relations linking cell growth and the cell cycle in Escherichia coli. Nature Microbiology, 5, 995–1001.

2019

Ma Z.#, Chu P.#, Su Y.#, Yu Y., Wen H., Fu X., Huang S.* (2019) Applications of single-cell technology on bacterial analysis. Quantitative Biology, 7(3).

Hillson N., Caddick M., Cai Y., Carrasco J., Chang M., Curach N., Bell D., Feuvre R., Friedman D., Fu X., Gold N., Herrgård M., Holowko M., Johnson J., Johnson R., Keasling J.D., Kitney R., Kondo A., Liu C., Martin V., Menolascina F., Ogino C., Patron N.J., Pavan M., Poh C., Pretorius I. S., Rosser S. J., Scrutton N. S., Storch M., Tekotte H., Travnik E., Vickers C. E., Yew W. S., Yuan Y., Zhao H., Freemont P. S. (2019) Building a global alliance of biofoundries. Nature Communications 10, 2040.

Chen L., Guan G., Liu Q., Yuan S., Yan T., Tian L., Zhou Y., Zhao Y., Ma Y., Wei T.*, Fu X.* (2019) Characterization and complete genomic analysis of two Salmonella phages, SenALZ1 and SenASZ3, new members of the genus Cba120virus. Archives of Virology. DOI:10.1007/s00705-019-04183-3.

2018

Cui J., Zhang B., Ma Y., Fu X., Wang M., Liu C. (2018) Engineering Platforms for Synthetic Biology Research. Bulletin of the Chinese Academy of Sciences 33(11):1249-1257.

Fu X.#, Kato S.#, Long J., Mattingly H. H., He C., Vural D. C., Zucker S. W., Emonet T. (2018) Spatial self-organization resolves conflicts between individuality and collective migration. Nature Communications 9, 2177.

2017

Bai Y., Gao M., Wen L., He C., Chen Y., Liu C., Fu X.*, Huang S.* (2017) Applications of Microfluidics in Quantitative Biology. Biotechnology Journal.

Liu L., Bai Y., Zheng H., Fu X., Liu C. (2017) Fundamental aspects of synthetic biology. Chinese Journal of Biotechnology (Chinese).

2015

Wang X., Liu C., Fu X., Huang J. (2015) Synthetic Biology: a New Means of Biological Pattern Formation Study. SCIENTIA SINICA Vitae (Chinese).

2014

Dufour Y.#, Fu X.#, Hernandez-Nunez L., Emonet T. (2014) Limits of Feedback Control in Bacterial Chemotaxis. PLoS Computational Biology.

Fu X., Huang W. (2014) Quantitative measurement and analysis in a synthetic pattern formation multicellular system. Methods in Molecular Biology.

2013

Liu C., Fu X., Huang J. D.* (2013) Synthetic biology: a new approach to study biological pattern formation. Quantitative Biology, 1, 7.

2012

Fu X., Tang L., Liu C., Huang J., Hwa T., Lenz P. (2012) Stripe formation in bacterial systems with density-suppressed motility. Physical Review Letters.

2011

Liu C.#, Fu X.#, Liu L., Ren X., Chau C. K., Li S., Xiang L., Zeng H., Chen G., Tang L. H., Lenz P., Cui X., Huang W., Hwa T., Huang J. D.* (2011) Sequential establishment of stripe patterns in an expanding cell population. Science 334, 238-241.